Starting phenix.real_space_refine on Thu Jul 31 08:43:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dyr_30923/07_2025/7dyr_30923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dyr_30923/07_2025/7dyr_30923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dyr_30923/07_2025/7dyr_30923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dyr_30923/07_2025/7dyr_30923.map" model { file = "/net/cci-nas-00/data/ceres_data/7dyr_30923/07_2025/7dyr_30923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dyr_30923/07_2025/7dyr_30923.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 8667 2.51 5 N 2229 2.21 5 O 2349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13326 Number of models: 1 Model: "" Number of chains: 12 Chain: "Y" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "Z" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "A" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "B" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "D" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "E" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "F" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "G" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.17, per 1000 atoms: 0.69 Number of scatterers: 13326 At special positions: 0 Unit cell: (120.954, 128.381, 85.941, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2349 8.00 N 2229 7.00 C 8667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 2.1 seconds 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 3 sheets defined 77.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR Y 37 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 61 removed outlier: 3.868A pdb=" N GLY Y 49 " --> pdb=" O ASP Y 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA Y 77 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 98 removed outlier: 3.542A pdb=" N LEU Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 117 Processing helix chain 'Y' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP Y 129 " --> pdb=" O ASP Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 143 Processing helix chain 'Y' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL Y 151 " --> pdb=" O GLN Y 147 " (cutoff:3.500A) Proline residue: Y 154 - end of helix removed outlier: 3.808A pdb=" N ALA Y 159 " --> pdb=" O ALA Y 155 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 171 removed outlier: 3.727A pdb=" N ASN Y 169 " --> pdb=" O SER Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN Y 183 " --> pdb=" O THR Y 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET Y 188 " --> pdb=" O ILE Y 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL Y 190 " --> pdb=" O GLY Y 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL Y 191 " --> pdb=" O GLY Y 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL Y 192 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY Y 193 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR Y 194 " --> pdb=" O VAL Y 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG Y 202 " --> pdb=" O ILE Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR Y 211 " --> pdb=" O MET Y 207 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR Y 220 " --> pdb=" O THR Y 216 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 241 Processing helix chain 'Z' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG Z 22 " --> pdb=" O GLN Z 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL Z 24 " --> pdb=" O ASP Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 31 No H-bonds generated for 'chain 'Z' and resid 29 through 31' Processing helix chain 'Z' and resid 41 through 49 Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG Z 55 " --> pdb=" O PRO Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 72 removed outlier: 3.594A pdb=" N HIS Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 99 Processing helix chain 'Z' and resid 106 through 127 removed outlier: 3.715A pdb=" N GLY Z 116 " --> pdb=" O VAL Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix removed outlier: 3.512A pdb=" N ASP Z 123 " --> pdb=" O ALA Z 119 " (cutoff:3.500A) Proline residue: Z 124 - end of helix Processing helix chain 'Z' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER Z 144 " --> pdb=" O GLY Z 140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY Z 145 " --> pdb=" O ILE Z 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Z 163 " --> pdb=" O LEU Z 159 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP Z 178 " --> pdb=" O SER Z 174 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL Z 180 " --> pdb=" O GLY Z 176 " (cutoff:3.500A) Processing helix chain 'Z' and resid 181 through 183 No H-bonds generated for 'chain 'Z' and resid 181 through 183' Processing helix chain 'Z' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS Z 190 " --> pdb=" O GLY Z 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN Z 208 " --> pdb=" O GLY Z 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR Z 211 " --> pdb=" O VAL Z 207 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 242 Processing helix chain 'Z' and resid 244 through 260 Processing helix chain 'Z' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE Z 267 " --> pdb=" O ASN Z 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 24 Processing helix chain 'A' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 3.868A pdb=" N GLY B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.543A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Proline residue: B 154 - end of helix removed outlier: 3.808A pdb=" N ALA B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 171 removed outlier: 3.726A pdb=" N ASN B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 192 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR B 211 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 Processing helix chain 'C' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.595A pdb=" N HIS C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 106 through 127 removed outlier: 3.715A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix removed outlier: 3.512A pdb=" N ASP C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 244 through 260 Processing helix chain 'C' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 61 removed outlier: 3.869A pdb=" N GLY E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 removed outlier: 3.542A pdb=" N LEU E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 143 Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL E 151 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Proline residue: E 154 - end of helix removed outlier: 3.808A pdb=" N ALA E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.726A pdb=" N ASN E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN E 183 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 192 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR E 211 " --> pdb=" O MET E 207 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR E 220 " --> pdb=" O THR E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 241 Processing helix chain 'F' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG F 22 " --> pdb=" O GLN F 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 41 through 49 Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 3.594A pdb=" N HIS F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 99 Processing helix chain 'F' and resid 106 through 127 removed outlier: 3.716A pdb=" N GLY F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Proline residue: F 117 - end of helix removed outlier: 3.512A pdb=" N ASP F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 163 " --> pdb=" O LEU F 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR F 211 " --> pdb=" O VAL F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 242 Processing helix chain 'F' and resid 244 through 260 Processing helix chain 'F' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE F 267 " --> pdb=" O ASN F 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 24 Processing helix chain 'G' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR Z 232 " --> pdb=" O VAL Z 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR C 232 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR F 232 " --> pdb=" O VAL F 219 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4269 1.34 - 1.46: 2665 1.46 - 1.58: 6509 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 13590 Sorted by residual: bond pdb=" N GLN F 41 " pdb=" CA GLN F 41 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.59e+00 bond pdb=" N GLN C 41 " pdb=" CA GLN C 41 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.22e+00 bond pdb=" CB PRO Z 132 " pdb=" CG PRO Z 132 " ideal model delta sigma weight residual 1.492 1.406 0.086 5.00e-02 4.00e+02 2.93e+00 bond pdb=" CB PRO C 132 " pdb=" CG PRO C 132 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.92e+00 bond pdb=" CB PRO F 132 " pdb=" CG PRO F 132 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.91e+00 ... (remaining 13585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17977 1.97 - 3.94: 413 3.94 - 5.91: 83 5.91 - 7.89: 16 7.89 - 9.86: 9 Bond angle restraints: 18498 Sorted by residual: angle pdb=" N VAL E 156 " pdb=" CA VAL E 156 " pdb=" C VAL E 156 " ideal model delta sigma weight residual 111.81 108.08 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" N VAL Y 156 " pdb=" CA VAL Y 156 " pdb=" C VAL Y 156 " ideal model delta sigma weight residual 111.81 108.08 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" N VAL B 156 " pdb=" CA VAL B 156 " pdb=" C VAL B 156 " ideal model delta sigma weight residual 111.81 108.09 3.72 8.60e-01 1.35e+00 1.87e+01 angle pdb=" C GLN Z 41 " pdb=" CA GLN Z 41 " pdb=" CB GLN Z 41 " ideal model delta sigma weight residual 111.48 105.78 5.70 1.59e+00 3.96e-01 1.29e+01 angle pdb=" CA TYR A 73 " pdb=" CB TYR A 73 " pdb=" CG TYR A 73 " ideal model delta sigma weight residual 113.90 107.46 6.44 1.80e+00 3.09e-01 1.28e+01 ... (remaining 18493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7076 17.78 - 35.56: 650 35.56 - 53.34: 194 53.34 - 71.12: 29 71.12 - 88.90: 4 Dihedral angle restraints: 7953 sinusoidal: 2979 harmonic: 4974 Sorted by residual: dihedral pdb=" CA ILE B 174 " pdb=" C ILE B 174 " pdb=" N PRO B 175 " pdb=" CA PRO B 175 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ILE E 174 " pdb=" C ILE E 174 " pdb=" N PRO E 175 " pdb=" CA PRO E 175 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE Y 174 " pdb=" C ILE Y 174 " pdb=" N PRO Y 175 " pdb=" CA PRO Y 175 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 7950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1715 0.052 - 0.104: 424 0.104 - 0.157: 78 0.157 - 0.209: 8 0.209 - 0.261: 1 Chirality restraints: 2226 Sorted by residual: chirality pdb=" CA ASP Z 103 " pdb=" N ASP Z 103 " pdb=" C ASP Z 103 " pdb=" CB ASP Z 103 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO B 72 " pdb=" N PRO B 72 " pdb=" C PRO B 72 " pdb=" CB PRO B 72 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA PRO Y 72 " pdb=" N PRO Y 72 " pdb=" C PRO Y 72 " pdb=" CB PRO Y 72 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 2223 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA Y 71 " 0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO Y 72 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Y 72 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO Y 72 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 71 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 72 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 71 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO E 72 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 72 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 72 " -0.050 5.00e-02 4.00e+02 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2180 2.74 - 3.28: 13533 3.28 - 3.82: 22248 3.82 - 4.36: 26647 4.36 - 4.90: 46236 Nonbonded interactions: 110844 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 125 " pdb=" NH2 ARG Z 39 " model vdw 2.205 3.120 nonbonded pdb=" OD2 ASP E 125 " pdb=" NH2 ARG F 39 " model vdw 2.205 3.120 nonbonded pdb=" OD2 ASP B 125 " pdb=" NH2 ARG C 39 " model vdw 2.206 3.120 nonbonded pdb=" N ASN G 67 " pdb=" OD1 ASN G 67 " model vdw 2.275 3.120 nonbonded pdb=" N ASN D 67 " pdb=" OD1 ASN D 67 " model vdw 2.275 3.120 ... (remaining 110839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'Y' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 34.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 13590 Z= 0.325 Angle : 0.779 9.857 18498 Z= 0.420 Chirality : 0.047 0.261 2226 Planarity : 0.006 0.091 2328 Dihedral : 15.368 88.905 4797 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.22 % Favored : 92.50 % Rotamer: Outliers : 3.56 % Allowed : 20.33 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1773 helix: 0.95 (0.15), residues: 1290 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 138 HIS 0.004 0.001 HIS Y 122 PHE 0.011 0.001 PHE C 47 TYR 0.027 0.003 TYR A 73 ARG 0.004 0.000 ARG Z 54 Details of bonding type rmsd hydrogen bonds : bond 0.14245 ( 888) hydrogen bonds : angle 5.94953 ( 2664) covalent geometry : bond 0.00776 (13590) covalent geometry : angle 0.77939 (18498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 1.496 Fit side-chains REVERT: Y 26 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7372 (mm-30) REVERT: Y 64 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7793 (mtp) REVERT: Y 125 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: Y 176 GLU cc_start: 0.7067 (tp30) cc_final: 0.6789 (tm-30) REVERT: Z 17 THR cc_start: 0.7504 (m) cc_final: 0.7291 (p) REVERT: Z 38 GLU cc_start: 0.8653 (tt0) cc_final: 0.7953 (tt0) REVERT: Z 60 ASN cc_start: 0.6699 (m-40) cc_final: 0.6131 (t0) REVERT: Z 73 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6989 (mt-10) REVERT: Z 94 GLU cc_start: 0.7693 (tt0) cc_final: 0.7217 (tt0) REVERT: Z 175 LYS cc_start: 0.7153 (tptm) cc_final: 0.6931 (tptp) REVERT: Z 223 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7239 (m) REVERT: Z 230 HIS cc_start: 0.7483 (m90) cc_final: 0.7028 (m90) REVERT: A 50 ASP cc_start: 0.6889 (m-30) cc_final: 0.6620 (m-30) REVERT: A 55 ASN cc_start: 0.8150 (p0) cc_final: 0.7944 (p0) REVERT: B 26 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 64 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: B 125 ASP cc_start: 0.7305 (m-30) cc_final: 0.6880 (m-30) REVERT: B 201 MET cc_start: 0.8138 (mtm) cc_final: 0.7772 (mtp) REVERT: C 15 LYS cc_start: 0.8126 (ptpp) cc_final: 0.7833 (ptpp) REVERT: C 17 THR cc_start: 0.7845 (m) cc_final: 0.7635 (p) REVERT: C 20 ASP cc_start: 0.7632 (m-30) cc_final: 0.7260 (m-30) REVERT: C 22 ARG cc_start: 0.6328 (mtp180) cc_final: 0.6116 (mtm110) REVERT: C 38 GLU cc_start: 0.8625 (tt0) cc_final: 0.8073 (tt0) REVERT: C 60 ASN cc_start: 0.6867 (m-40) cc_final: 0.6507 (t0) REVERT: C 73 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7205 (mt-10) REVERT: D 50 ASP cc_start: 0.7159 (m-30) cc_final: 0.6647 (m-30) REVERT: D 55 ASN cc_start: 0.8316 (p0) cc_final: 0.7979 (p0) REVERT: E 3 ILE cc_start: 0.7863 (mt) cc_final: 0.7514 (mm) REVERT: E 4 THR cc_start: 0.7488 (p) cc_final: 0.7264 (t) REVERT: E 130 ASN cc_start: 0.8118 (m110) cc_final: 0.7796 (m-40) REVERT: E 142 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8125 (p) REVERT: E 176 GLU cc_start: 0.7063 (tp30) cc_final: 0.6785 (tm-30) REVERT: E 180 ASN cc_start: 0.7838 (m-40) cc_final: 0.7495 (m-40) REVERT: E 244 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7980 (ttpp) REVERT: F 17 THR cc_start: 0.7743 (m) cc_final: 0.7460 (p) REVERT: F 38 GLU cc_start: 0.8654 (tt0) cc_final: 0.8036 (tt0) REVERT: F 60 ASN cc_start: 0.6881 (m-40) cc_final: 0.6221 (t0) REVERT: F 73 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7015 (mt-10) REVERT: F 95 GLN cc_start: 0.7180 (mp10) cc_final: 0.6768 (mp-120) REVERT: F 102 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6931 (mm) REVERT: F 108 ASN cc_start: 0.7986 (m-40) cc_final: 0.7752 (m-40) REVERT: F 189 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6427 (pt0) REVERT: F 193 GLU cc_start: 0.7609 (tt0) cc_final: 0.7397 (tt0) REVERT: F 259 ARG cc_start: 0.6852 (tpp80) cc_final: 0.6457 (ttp80) REVERT: F 281 CYS cc_start: 0.7790 (m) cc_final: 0.7579 (m) REVERT: G 19 TRP cc_start: 0.6334 (t60) cc_final: 0.6107 (t60) outliers start: 49 outliers final: 13 residues processed: 317 average time/residue: 1.3147 time to fit residues: 455.7058 Evaluate side-chains 241 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 64 MET Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 142 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 73 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 158 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 29 ASN A 15 ASN A 42 GLN C 108 ASN C 158 ASN D 15 ASN F 158 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.077204 restraints weight = 17968.516| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.68 r_work: 0.2896 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13590 Z= 0.156 Angle : 0.610 6.584 18498 Z= 0.323 Chirality : 0.042 0.166 2226 Planarity : 0.006 0.089 2328 Dihedral : 5.846 54.881 1970 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.20 % Favored : 93.63 % Rotamer: Outliers : 3.56 % Allowed : 17.36 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1773 helix: 1.31 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -2.30 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 127 HIS 0.003 0.001 HIS G 51 PHE 0.013 0.001 PHE C 157 TYR 0.024 0.002 TYR A 73 ARG 0.004 0.001 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 888) hydrogen bonds : angle 4.23524 ( 2664) covalent geometry : bond 0.00355 (13590) covalent geometry : angle 0.60959 (18498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: Y 125 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: Y 176 GLU cc_start: 0.7277 (tp30) cc_final: 0.7062 (tp30) REVERT: Z 60 ASN cc_start: 0.7165 (m-40) cc_final: 0.6732 (t0) REVERT: Z 94 GLU cc_start: 0.8842 (tt0) cc_final: 0.8450 (tt0) REVERT: Z 223 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7466 (m) REVERT: Z 230 HIS cc_start: 0.7989 (m90) cc_final: 0.7701 (m90) REVERT: Z 259 ARG cc_start: 0.8165 (ttm110) cc_final: 0.7964 (ttp80) REVERT: B 26 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8272 (mm-30) REVERT: B 244 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8513 (ttpp) REVERT: C 17 THR cc_start: 0.8705 (m) cc_final: 0.8502 (p) REVERT: C 20 ASP cc_start: 0.8758 (m-30) cc_final: 0.8544 (m-30) REVERT: C 38 GLU cc_start: 0.9028 (tt0) cc_final: 0.8774 (tt0) REVERT: C 60 ASN cc_start: 0.7187 (m-40) cc_final: 0.6953 (t0) REVERT: D 16 ASN cc_start: 0.8231 (m-40) cc_final: 0.7995 (m-40) REVERT: E 176 GLU cc_start: 0.7255 (tp30) cc_final: 0.6869 (tm-30) REVERT: F 38 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: F 95 GLN cc_start: 0.8405 (mp10) cc_final: 0.8061 (mp-120) REVERT: F 183 MET cc_start: 0.6529 (mmm) cc_final: 0.6283 (mmm) REVERT: F 189 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: G 19 TRP cc_start: 0.6720 (t60) cc_final: 0.6407 (t60) outliers start: 49 outliers final: 16 residues processed: 271 average time/residue: 1.6480 time to fit residues: 485.8000 Evaluate side-chains 234 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 126 LYS Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 165 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 121 GLN Z 36 ASN A 11 ASN A 15 ASN C 108 ASN D 11 ASN D 15 ASN E 121 GLN F 29 ASN F 36 ASN F 108 ASN F 158 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.075253 restraints weight = 17999.995| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.68 r_work: 0.2860 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13590 Z= 0.167 Angle : 0.610 7.965 18498 Z= 0.323 Chirality : 0.043 0.177 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.417 58.326 1954 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.98 % Favored : 93.85 % Rotamer: Outliers : 3.41 % Allowed : 17.43 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1773 helix: 1.45 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -2.41 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 127 HIS 0.003 0.001 HIS B 140 PHE 0.012 0.001 PHE F 47 TYR 0.026 0.002 TYR A 73 ARG 0.003 0.000 ARG Y 114 Details of bonding type rmsd hydrogen bonds : bond 0.05212 ( 888) hydrogen bonds : angle 4.10897 ( 2664) covalent geometry : bond 0.00391 (13590) covalent geometry : angle 0.60968 (18498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: Y 125 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: Y 176 GLU cc_start: 0.7510 (tp30) cc_final: 0.7158 (tp30) REVERT: Z 60 ASN cc_start: 0.7152 (m-40) cc_final: 0.6737 (t0) REVERT: Z 94 GLU cc_start: 0.8838 (tt0) cc_final: 0.8476 (tt0) REVERT: Z 223 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7468 (m) REVERT: Z 230 HIS cc_start: 0.7994 (m90) cc_final: 0.7713 (m90) REVERT: B 26 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8253 (mm-30) REVERT: C 38 GLU cc_start: 0.9034 (tt0) cc_final: 0.8790 (tt0) REVERT: D 16 ASN cc_start: 0.8236 (m-40) cc_final: 0.8010 (m-40) REVERT: D 29 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5935 (tm) REVERT: E 176 GLU cc_start: 0.7322 (tp30) cc_final: 0.6998 (tm-30) REVERT: F 38 GLU cc_start: 0.9133 (tt0) cc_final: 0.8881 (tt0) REVERT: F 95 GLN cc_start: 0.8413 (mp10) cc_final: 0.8061 (mp-120) REVERT: F 183 MET cc_start: 0.6690 (mmm) cc_final: 0.6398 (mmm) REVERT: F 189 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: G 19 TRP cc_start: 0.6705 (t60) cc_final: 0.6402 (t60) outliers start: 47 outliers final: 21 residues processed: 276 average time/residue: 1.2976 time to fit residues: 390.2719 Evaluate side-chains 250 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 101 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN A 15 ASN A 42 GLN C 98 ASN C 108 ASN D 11 ASN D 15 ASN F 36 ASN F 108 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 15 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.075315 restraints weight = 17940.936| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.69 r_work: 0.2858 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13590 Z= 0.164 Angle : 0.601 6.665 18498 Z= 0.319 Chirality : 0.042 0.175 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.474 58.201 1954 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 3.27 % Allowed : 18.30 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1773 helix: 1.53 (0.15), residues: 1314 sheet: None (None), residues: 0 loop : -2.46 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 PHE 0.012 0.001 PHE F 47 TYR 0.026 0.002 TYR A 73 ARG 0.003 0.000 ARG E 150 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 888) hydrogen bonds : angle 4.02415 ( 2664) covalent geometry : bond 0.00383 (13590) covalent geometry : angle 0.60137 (18498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: Y 58 MET cc_start: 0.9104 (mmm) cc_final: 0.8633 (mmp) REVERT: Y 125 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: Y 176 GLU cc_start: 0.7468 (tp30) cc_final: 0.7201 (tp30) REVERT: Z 94 GLU cc_start: 0.8810 (tt0) cc_final: 0.8470 (tt0) REVERT: Z 223 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7434 (m) REVERT: Z 230 HIS cc_start: 0.7974 (m90) cc_final: 0.7671 (m90) REVERT: B 26 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8228 (mm-30) REVERT: B 166 GLU cc_start: 0.6555 (pm20) cc_final: 0.6298 (pm20) REVERT: B 170 MET cc_start: 0.6978 (ttm) cc_final: 0.6769 (mtm) REVERT: C 38 GLU cc_start: 0.9038 (tt0) cc_final: 0.8822 (tt0) REVERT: D 16 ASN cc_start: 0.8170 (m-40) cc_final: 0.7937 (m-40) REVERT: D 29 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6129 (tm) REVERT: E 64 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8659 (mtp) REVERT: E 176 GLU cc_start: 0.7220 (tp30) cc_final: 0.7016 (tm-30) REVERT: F 38 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8905 (tt0) REVERT: F 95 GLN cc_start: 0.8366 (mp10) cc_final: 0.7985 (mp-120) REVERT: F 183 MET cc_start: 0.6703 (mmm) cc_final: 0.6408 (mmm) REVERT: F 189 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: G 19 TRP cc_start: 0.6764 (t60) cc_final: 0.6401 (t60) outliers start: 45 outliers final: 25 residues processed: 263 average time/residue: 1.1959 time to fit residues: 342.8896 Evaluate side-chains 255 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 128 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 163 optimal weight: 0.2980 chunk 142 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN Z 60 ASN A 15 ASN B 180 ASN C 98 ASN C 108 ASN D 11 ASN D 15 ASN F 36 ASN F 108 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 15 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.101215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.076408 restraints weight = 17991.737| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.68 r_work: 0.2876 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13590 Z= 0.146 Angle : 0.581 7.945 18498 Z= 0.307 Chirality : 0.041 0.165 2226 Planarity : 0.005 0.086 2328 Dihedral : 5.448 58.473 1954 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 2.98 % Allowed : 18.16 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1773 helix: 1.71 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.46 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 PHE 0.013 0.001 PHE F 47 TYR 0.024 0.002 TYR A 73 ARG 0.002 0.000 ARG E 150 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 888) hydrogen bonds : angle 3.93882 ( 2664) covalent geometry : bond 0.00334 (13590) covalent geometry : angle 0.58139 (18498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: Y 58 MET cc_start: 0.9121 (mmm) cc_final: 0.8587 (mmp) REVERT: Y 125 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: Y 176 GLU cc_start: 0.7400 (tp30) cc_final: 0.7167 (tp30) REVERT: Z 36 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.7974 (p0) REVERT: Z 223 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7404 (m) REVERT: Z 230 HIS cc_start: 0.8012 (m90) cc_final: 0.7679 (m90) REVERT: A 29 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.6128 (tm) REVERT: B 26 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8219 (mm-30) REVERT: C 38 GLU cc_start: 0.9015 (tt0) cc_final: 0.8804 (tt0) REVERT: D 16 ASN cc_start: 0.8160 (m-40) cc_final: 0.7921 (m-40) REVERT: D 29 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6177 (tm) REVERT: E 176 GLU cc_start: 0.7244 (tp30) cc_final: 0.7020 (tm-30) REVERT: F 36 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8044 (p0) REVERT: F 38 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8894 (tt0) REVERT: F 95 GLN cc_start: 0.8390 (mp10) cc_final: 0.8035 (mp-120) REVERT: F 183 MET cc_start: 0.6668 (mmm) cc_final: 0.6402 (mmm) REVERT: F 189 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: G 19 TRP cc_start: 0.6829 (t60) cc_final: 0.6446 (t60) outliers start: 41 outliers final: 23 residues processed: 261 average time/residue: 1.3901 time to fit residues: 398.1047 Evaluate side-chains 253 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 2 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 143 optimal weight: 0.9990 chunk 41 optimal weight: 0.0010 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN Z 60 ASN A 15 ASN C 98 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 15 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.076034 restraints weight = 18158.370| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.70 r_work: 0.2872 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13590 Z= 0.151 Angle : 0.590 10.369 18498 Z= 0.311 Chirality : 0.042 0.170 2226 Planarity : 0.006 0.086 2328 Dihedral : 5.429 56.527 1954 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 3.27 % Allowed : 18.59 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1773 helix: 1.77 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.43 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 PHE 0.013 0.001 PHE F 47 TYR 0.025 0.002 TYR A 73 ARG 0.003 0.000 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 888) hydrogen bonds : angle 3.92762 ( 2664) covalent geometry : bond 0.00351 (13590) covalent geometry : angle 0.59024 (18498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8246 (mtmt) REVERT: Y 58 MET cc_start: 0.9126 (mmm) cc_final: 0.8556 (mmp) REVERT: Y 125 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: Y 176 GLU cc_start: 0.7445 (tp30) cc_final: 0.7231 (tp30) REVERT: Y 244 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8488 (ttpp) REVERT: Z 36 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8101 (p0) REVERT: Z 187 PHE cc_start: 0.8146 (t80) cc_final: 0.7935 (t80) REVERT: Z 223 THR cc_start: 0.7716 (OUTLIER) cc_final: 0.7361 (m) REVERT: Z 230 HIS cc_start: 0.8005 (m90) cc_final: 0.7665 (m90) REVERT: A 29 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.6082 (tm) REVERT: B 26 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8208 (mm-30) REVERT: B 47 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8236 (tttp) REVERT: D 16 ASN cc_start: 0.8166 (m-40) cc_final: 0.7919 (m-40) REVERT: D 29 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6059 (tm) REVERT: E 176 GLU cc_start: 0.7354 (tp30) cc_final: 0.7083 (tm-30) REVERT: F 36 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8004 (p0) REVERT: F 38 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8870 (tt0) REVERT: F 95 GLN cc_start: 0.8374 (mp10) cc_final: 0.8024 (mp-120) REVERT: F 183 MET cc_start: 0.6679 (mmm) cc_final: 0.6408 (mmm) REVERT: F 189 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: G 19 TRP cc_start: 0.6872 (t60) cc_final: 0.6472 (t60) outliers start: 45 outliers final: 23 residues processed: 266 average time/residue: 1.3411 time to fit residues: 391.5519 Evaluate side-chains 259 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 0.0970 chunk 124 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 40 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN Z 60 ASN Z 189 GLN A 15 ASN C 71 HIS C 98 ASN C 108 ASN D 11 ASN D 15 ASN F 36 ASN F 108 ASN F 189 GLN G 11 ASN G 15 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.077857 restraints weight = 18077.549| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.68 r_work: 0.2902 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13590 Z= 0.133 Angle : 0.568 9.693 18498 Z= 0.299 Chirality : 0.041 0.154 2226 Planarity : 0.005 0.084 2328 Dihedral : 5.390 59.501 1954 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 3.27 % Allowed : 18.52 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.21), residues: 1773 helix: 1.90 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.41 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 127 HIS 0.002 0.001 HIS B 140 PHE 0.012 0.001 PHE F 47 TYR 0.020 0.001 TYR D 73 ARG 0.002 0.000 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 888) hydrogen bonds : angle 3.85410 ( 2664) covalent geometry : bond 0.00296 (13590) covalent geometry : angle 0.56789 (18498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8256 (mtmt) REVERT: Y 58 MET cc_start: 0.9117 (mmm) cc_final: 0.8521 (mmp) REVERT: Y 244 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8321 (ttpp) REVERT: Z 36 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8179 (p0) REVERT: Z 66 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8237 (mt0) REVERT: Z 187 PHE cc_start: 0.8119 (t80) cc_final: 0.7888 (t80) REVERT: Z 223 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7415 (m) REVERT: Z 230 HIS cc_start: 0.7999 (m90) cc_final: 0.7665 (m90) REVERT: A 29 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6202 (tm) REVERT: B 26 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8181 (mm-30) REVERT: B 47 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8233 (tttp) REVERT: B 244 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8419 (ptpp) REVERT: D 16 ASN cc_start: 0.8139 (m-40) cc_final: 0.7890 (m-40) REVERT: D 29 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6108 (tm) REVERT: E 47 LYS cc_start: 0.8653 (mmmm) cc_final: 0.8439 (tttt) REVERT: E 176 GLU cc_start: 0.7273 (tp30) cc_final: 0.6987 (tm-30) REVERT: F 36 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8082 (p0) REVERT: F 38 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8875 (tt0) REVERT: F 95 GLN cc_start: 0.8378 (mp10) cc_final: 0.8024 (mp-120) REVERT: F 183 MET cc_start: 0.6655 (mmm) cc_final: 0.6396 (mmm) REVERT: F 189 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: G 19 TRP cc_start: 0.6875 (t60) cc_final: 0.6496 (t60) outliers start: 45 outliers final: 22 residues processed: 264 average time/residue: 1.1969 time to fit residues: 345.9255 Evaluate side-chains 256 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN Z 60 ASN A 15 ASN B 130 ASN C 98 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.076233 restraints weight = 18085.607| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.69 r_work: 0.2873 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13590 Z= 0.155 Angle : 0.598 10.224 18498 Z= 0.314 Chirality : 0.042 0.168 2226 Planarity : 0.005 0.083 2328 Dihedral : 5.239 59.589 1952 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 3.20 % Allowed : 18.81 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1773 helix: 1.89 (0.15), residues: 1323 sheet: None (None), residues: 0 loop : -2.49 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 PHE 0.014 0.001 PHE F 47 TYR 0.025 0.002 TYR A 73 ARG 0.002 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 888) hydrogen bonds : angle 3.89870 ( 2664) covalent geometry : bond 0.00358 (13590) covalent geometry : angle 0.59794 (18498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8287 (mtmt) REVERT: Y 244 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8441 (ttpp) REVERT: Z 36 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8209 (p0) REVERT: Z 61 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7202 (p0) REVERT: Z 66 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8225 (mt0) REVERT: Z 187 PHE cc_start: 0.8131 (t80) cc_final: 0.7903 (t80) REVERT: Z 223 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7406 (m) REVERT: Z 230 HIS cc_start: 0.7997 (m90) cc_final: 0.7610 (m90) REVERT: A 29 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6236 (tm) REVERT: B 26 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8165 (mm-30) REVERT: B 47 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8245 (tttp) REVERT: D 16 ASN cc_start: 0.8098 (m-40) cc_final: 0.7792 (m-40) REVERT: D 29 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6048 (tm) REVERT: E 176 GLU cc_start: 0.7329 (tp30) cc_final: 0.7084 (tm-30) REVERT: F 36 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8107 (p0) REVERT: F 38 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8871 (tt0) REVERT: F 95 GLN cc_start: 0.8366 (mp10) cc_final: 0.8000 (mp-120) REVERT: F 183 MET cc_start: 0.6680 (mmm) cc_final: 0.6410 (mmm) REVERT: F 189 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: G 19 TRP cc_start: 0.6844 (t60) cc_final: 0.6438 (t60) outliers start: 44 outliers final: 20 residues processed: 261 average time/residue: 1.1566 time to fit residues: 330.4616 Evaluate side-chains 255 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 7 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 165 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN Z 60 ASN Z 189 GLN A 15 ASN C 98 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.075512 restraints weight = 17912.673| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.68 r_work: 0.2860 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13590 Z= 0.168 Angle : 0.620 10.826 18498 Z= 0.326 Chirality : 0.043 0.177 2226 Planarity : 0.006 0.083 2328 Dihedral : 5.276 59.399 1952 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.15 % Favored : 93.68 % Rotamer: Outliers : 2.98 % Allowed : 18.88 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1773 helix: 1.86 (0.15), residues: 1323 sheet: None (None), residues: 0 loop : -2.45 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 PHE 0.015 0.001 PHE F 47 TYR 0.027 0.002 TYR A 73 ARG 0.003 0.000 ARG Z 39 Details of bonding type rmsd hydrogen bonds : bond 0.04963 ( 888) hydrogen bonds : angle 3.93995 ( 2664) covalent geometry : bond 0.00397 (13590) covalent geometry : angle 0.61982 (18498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 2.426 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8333 (mtmt) REVERT: Y 58 MET cc_start: 0.9085 (mmm) cc_final: 0.8519 (mmp) REVERT: Y 244 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8327 (ttpp) REVERT: Z 36 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.7887 (p0) REVERT: Z 61 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7254 (p0) REVERT: Z 66 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8237 (mt0) REVERT: Z 187 PHE cc_start: 0.8145 (t80) cc_final: 0.7925 (t80) REVERT: Z 223 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7366 (m) REVERT: Z 230 HIS cc_start: 0.7992 (m90) cc_final: 0.7731 (m-70) REVERT: B 26 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8203 (mm-30) REVERT: B 47 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8271 (tttp) REVERT: D 16 ASN cc_start: 0.8132 (m-40) cc_final: 0.7851 (m-40) REVERT: D 29 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6166 (tm) REVERT: F 36 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8036 (p0) REVERT: F 38 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8857 (tt0) REVERT: F 95 GLN cc_start: 0.8372 (mp10) cc_final: 0.8030 (mp-120) REVERT: F 183 MET cc_start: 0.6659 (mmm) cc_final: 0.6389 (mmm) REVERT: F 189 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: G 19 TRP cc_start: 0.6834 (t60) cc_final: 0.6408 (t60) outliers start: 41 outliers final: 17 residues processed: 257 average time/residue: 1.6988 time to fit residues: 477.5842 Evaluate side-chains 250 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 80 optimal weight: 0.0980 chunk 142 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN Z 60 ASN A 15 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.077151 restraints weight = 17985.782| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.68 r_work: 0.2891 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13590 Z= 0.141 Angle : 0.592 11.081 18498 Z= 0.311 Chirality : 0.041 0.168 2226 Planarity : 0.005 0.083 2328 Dihedral : 5.189 58.816 1952 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.64 % Favored : 94.19 % Rotamer: Outliers : 2.40 % Allowed : 19.75 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1773 helix: 1.94 (0.15), residues: 1323 sheet: None (None), residues: 0 loop : -2.45 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 127 HIS 0.002 0.001 HIS B 140 PHE 0.012 0.001 PHE F 47 TYR 0.022 0.002 TYR A 73 ARG 0.003 0.000 ARG Z 39 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 888) hydrogen bonds : angle 3.86699 ( 2664) covalent geometry : bond 0.00317 (13590) covalent geometry : angle 0.59222 (18498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8346 (mtmt) REVERT: Y 58 MET cc_start: 0.9068 (mmm) cc_final: 0.8639 (mmp) REVERT: Y 176 GLU cc_start: 0.7521 (tp30) cc_final: 0.7319 (tt0) REVERT: Y 244 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8316 (ttpp) REVERT: Z 36 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8160 (p0) REVERT: Z 66 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8229 (mt0) REVERT: Z 187 PHE cc_start: 0.8134 (t80) cc_final: 0.7902 (t80) REVERT: Z 223 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7378 (m) REVERT: Z 230 HIS cc_start: 0.7991 (m90) cc_final: 0.7585 (m90) REVERT: B 26 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8184 (mm-30) REVERT: B 47 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8290 (tttp) REVERT: D 16 ASN cc_start: 0.8114 (m-40) cc_final: 0.7791 (m-40) REVERT: D 29 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6204 (tm) REVERT: E 176 GLU cc_start: 0.7410 (tt0) cc_final: 0.7171 (tm-30) REVERT: F 36 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8078 (p0) REVERT: F 38 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8871 (tt0) REVERT: F 95 GLN cc_start: 0.8404 (mp10) cc_final: 0.8067 (mp-120) REVERT: F 183 MET cc_start: 0.6703 (mmm) cc_final: 0.6410 (mmm) REVERT: F 189 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: G 19 TRP cc_start: 0.6826 (t60) cc_final: 0.6411 (t60) outliers start: 33 outliers final: 20 residues processed: 249 average time/residue: 1.5337 time to fit residues: 417.0846 Evaluate side-chains 252 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 40 MET Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 130 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.0470 chunk 125 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN Z 60 ASN A 15 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN G 42 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.076115 restraints weight = 18037.701| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.68 r_work: 0.2870 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13590 Z= 0.158 Angle : 0.613 10.827 18498 Z= 0.323 Chirality : 0.042 0.171 2226 Planarity : 0.005 0.080 2328 Dihedral : 5.201 58.124 1952 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 2.54 % Allowed : 20.04 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1773 helix: 1.90 (0.15), residues: 1323 sheet: None (None), residues: 0 loop : -2.31 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 127 HIS 0.003 0.001 HIS B 140 PHE 0.014 0.001 PHE F 47 TYR 0.026 0.002 TYR A 73 ARG 0.004 0.000 ARG Z 39 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 888) hydrogen bonds : angle 3.90287 ( 2664) covalent geometry : bond 0.00366 (13590) covalent geometry : angle 0.61334 (18498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12924.57 seconds wall clock time: 229 minutes 24.67 seconds (13764.67 seconds total)